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<h1 align="center">VGLII - Virtual Genetics  version II</h1>
<a href="#The Goals and Objectives of the Lab">The Goals and Objectives of the Lab</a>
<br>
<a href="#The Genetic Models found in VGL">The Genetic Models found in VGLII</a>
<br>
<a href="#Running VGL - Virtual Genetics Lab">Running VGLII - Virtual Genetics Lab II</a>
<br>
<a href="#How To Start A New Problem">How To Start A New Problem</a>
<br>
<a href="#Cages in Regular Mode">Cages in Regular Mode</a>
<br>
<a href="#Cages in Practice Mode">Cages in Practice Mode</a>
<br>
<a href="#How To Open Work You have Saved Previously">How To Open Work You have Saved Previously</a>
<br>
<a href="#How to Save Work in Progress">How to Save Work in Progress</a>
<br>
<a href="#How to Save Your Work Under A Different Name">How to Save Your Work Under A Different Name</a>
<br>
<a href="#How to Close A Problem in Progress">How to Close A Problem in Progress</a>
<br>
<a href="#How to Cross Two Organisms">How to Cross Two Organisms</a>
<br>
<a href="#How to Print">How to print the work you have done so far</a>
<br>
<a href="#How to Print to File">How to Print to File</a>
<br>
<a href="#Summarize Cages">How to summarize the results from a set of cages</a>
<br>
<a href="#Close/Re-open Cages">Close/Re-open Cages</a>
<br>
<a href="#Re-arrange Cages">Re-arrange Cages</a>
<br>
<a href="#How to Get Details about each Phenotype">How to Get Details about each Phenotype</a>
<br>
<a href="#How to Get Details about VGL">How to Get Details about VGLII</a>
<br>
<br>
<hr>
<br>
<a name="The Goals and Objectives of the Lab"></a><font color="purple"><i>The Goals and Objectives of the Lab</i></font>
<br>
<p >
	When you start the problem you are given a cage of a population of creatures collected in the 
	field. Each of these creatures will display one of two to six different <i>traits</i> 
	of one to three particular <i>characters</i> (for example, if the character is Body Color, the traits 
	might be Red Body and Green Body). Your task is to discover how these characters are inherited. 
	You determine this by <a href="#How to Cross Two Organisms">crossing</a> particular individuals 
	and observing their offspring.  You then
	use the resulting data to deduce the underlying <a href="#The Genetic Models found in VGL">
	genetic models</a> that determines the inheritance of these characters.  <font color="purple">You</font> 
	must decide when 
	you have collected enough information to be convinced that you are right - the program will 
	not tell you the right answer (except when in <a href="#Cages in Practice Mode">Practice Mode</a>).
	</p>
<p >
	When you start a new problem, VGLII randomly chooses one to three characters from a list of possible 
	characters.
	It then randomly chooses <a href="#The Genetic Models found in VGL">genetic models</a> from a list of 
	possible genetic models.  The range of possible models is be custom-configured by your 
	instructor when she creates a problem type; different problem types can have greater or
	fewer possible models and <a href="#Practice Mode">Practice Mode</a> can be enabled or disabled
	for a particular problem type. <font color="purple">Since this assignment is random, the same character
	can be inherited in different ways in different problems.</font>
	</p>
<p >
	Next, VGLII chooses particular traits of each character and assigns them randomly
	to particular genotypes.  A population of individuals with random genotypes is then generated;
	these individuals are placed in Cage 1.
	</p>
<p >
	Your task is to <a href="#How to Cross Two Organisms">cross</a> individuals from different 
	cages and observe the resulting offspring.
	From these data, you will determine the <a href="#The Genetic Models found in VGL">genetic 
	models</a> of how your particular characters are inherited.
	</p>
<br>
<a name="The Genetic Models found in VGLII"></a><font color="purple"><i>The Genetic Models found in VGL</i></font>
<br>
<p >
	All the problems in VGLII involve genetic models with genes that have either two 
	or three alleles.  Based on 
	this, there are several features that can vary:<br>
	<ul>
      <li><b>The number of alleles</b>.  This can be either:</li>
        <ul>
          <li><u>Two alleles</u>.  In this case, there are two possible ways 
            these alleles can interact:</li>
			<ul>
			  <li><i>Simple Dominance</i>: The heterozygote has the same 
					phenotype as the dominant homozygote.  That is, with two alleles A and a:</li>
			    <ul>
				  <li>AA = tall</li>
				  <li>Aa = tall</li>
				  <li>aa = short</li>
				</ul>
			  <li><i>Incomplete Dominance</i>: The heterozygote has a 
					different phenotype than either homozygote.  In nature, this is usually 
					intermediate; in VGL it need not be.</li>
			    <ul>
				  <li>AA = tall</li>
				  <li>Aa = medium</li>
				  <li>aa = short</li>
				</ul>
			</ul>
      <li><u>Three alleles</u>.  In this case, there are two different possible
        ways these alleles can interact:</li>
        <ul>
          <li><i>Hierarchical dominance</i>:  A is dominant to B and C;
            B is dominant to C; C is reccessive to all.</li>
            <ul>
              <li>AA = green</li>
              <li>AB = green</li>
              <li>AC = green</li>
              <li>BB = red</li>
              <li>BC = red</li>
              <li>CC = blue</li>
            </ul>
          <li><i>Circular dominance</i>:  A is dominant to B;
            B is dominant to C; C is dominant to A.</li>
            <ul>
              <li>AA = green</li>
              <li>AB = green</li>
              <li>AC = blue</li>
              <li>BB = red</li>
              <li>BC = red</li>
              <li>CC = blue</li>
            </ul>
        </ul>
     </ul>          
		<li><b>Whether the character is sex-linked or not</b>; this can be either:</li>
			<ul>
				<li><u>Not sex-linked</u> - the gene for the character is carried on an autosome
					so it is inherited identically in both sexes.</li>
				<li><u>Sex-linked</u> - the gene for the character is located on a sex-chromosome
					so it is inherited differently in different sexes. This has two forms:</li>
					<ul>
						<li><i>XX/XY</i> Females are XX; males are XY.
							Here, Y carries no genes except those needed to make the organism male.</li>
						<li><i>ZZ/ZW</i> Females are ZW; males are ZZ.
							Here, W carries no genes except those needed to make the organism female.</li>
					</ul>
			</ul>
			<li><b>If genes on the same chromosome are linked or not</b>; the recombination
			       frequency can vary between 0% (completely linked) and 50% (completely unlinked).</li>
		</ul>
	</p>
<p >
<br>		
	</p>
		
						
				
<a name="Running VGL - Virtual Genetics Lab"></a><font color="purple">
<i>Running VGLII - Virtual Genetics Lab</i></font>
<br>
<p >To run VGLII simply double-click on the VGLIIx.x file.
		Note: Be sure to have the Problems folder in the same 
		folder as the VGLIIx.x file.  The toolbar buttons are shown below:
		</p>
<img src="fig0.gif">
<br>
<a name="How To Start A New Problem"></a><font color="purple"><i>How To Start A New Problem</i></font>
<br>
<p >When you start VGLII, you will see a toolbar like this:<br>
		<img src="fig1.jpg"><br>
		From the "File" menu, select "New Problem" or simply click on the "New Problem" button on the 
		toolbar and you will see a list of problem type files. The files are listed in increasing
		order of difficulty.  Additional problem type files can be generated using the VGLAdmin
		program.  Select the file and click on the "Open" button. 
		</p>
<p >
		 Once you start a problem, a window (Cage 1) will be opened up on the screen.  
		This cage is the starting point for your project.  The organisms can be, but are not
		necessarily, pure-breeding.
		</p>
<br>
<a name="Cages in Regular Mode"></a><font color="purple"><i>Cages in Regular Mode</i></font>
<br>
One cage in Regular Mode is Shown below:<br>
<img src="fig2.jpg"><br>
A sequence of <a href="#How to Cross Two Organisms">crosses</a> is shown below:<br>
<img src="fig3.jpg"><br>
This would be written out as:<br>
<pre>
Cross 1: 
Parents:	Five/Red male from Cage 1 <font color="purple">X</font> Five/Blue female from Cage 1

Offspring:				11 Five/Blue
(in Cage 2)				16 Five/Red

</pre>
 <br><br>

<a name="Cages in Practice Mode"></a><font color="purple"><i>Cages in Practice Mode</i></font>
<br>
If your instructor has enabled Practice mode for a particular problem, you will be able to
see details of the &quot;answer&quot; - the genetic model for each character and the genotype
of each organism.<p>
<p >In practice mode, a cage will look like this:<br>
	<img src="fig4.jpg"><br>
	This is the same as in Regular Mode, except that the model and genotypes can be seen.
	</p>
<br>
<a name="How To Open Work You have Saved Previously"></a><font color="purple"><i>How To Open Work You have Saved Previously</i></font>
<br>
<p ><img src="../images/open.gif">You can use this feature to load up previously saved problems that you might have been
		working on. To open a problem you can either select "Open Problem" from the drop-down
		"File" menu or simply click on the "Open Problem" button on the toolbar. A dialog box
		will open up to assist you in selecting a file. Browse to the directory in which the
		problem file is stored. Select the file and click on the "Open" button. VGLII will read
		the file and will open up the problem and bring it in the state* you last left it in 
		before you saved and closed the problem.<br><br>

		*state - state in this context is defined as the entire collection of cages created by
		the user, including cages that were created by the user but were kept closed during the
		course of problem work. Simply stated, this means that when you open a problem, VGLII
		will display all the cages created by you up until the point you closed the problem.
		</p>
<br>
<a name="How to Save Work in Progress"></a><font color="purple"><i>How to Save Work in Progress</i></font>
<br>
<p ><img src="../images/save.gif">You can use this feature to save your current work to a file. To save your work you can
either select "Save" from the drop-down "File" menu or simply click on the "Save" button
on the toolbar. A dialog box will open up to assist you in saving your work to a file in
the directory of your choice. Browse to the directory in which you want to save your work.
in the "File Name" field enter the name of the file you want you want to save your work
as. Then click on the "Open" button. This will create and open a file with the name 
as specified in the field and will store your current work in it. The file will have a
.wrk extension.
		</p>
<br>
<a name="How to Save Your Work Under A Different Name"></a><font color="purple"><i>How to Save Your Work Under A Different Name</i></font>
<br>
<p ><img src="../images/saveas.gif">This is the same as "Save a Problem" except that it creates a copy of the file you have
already created but with a different name.
		</p>
<br>
<a name="How to Close A Problem in Progress"></a><font color="purple"><i>How to Close A Problem in Progress</i></font>
<br>
<p ><img src="../images/closework.gif">You can use this feature to close a problem that you have been working on. To close the
problem that you have been working on select "Close Problem" from the "File" menu or simply
click the Close button on the toolbar. A
dialog box will pop-up to confirm your decision to close the problem. If you select "Yes"
and if you have any unsaved work then the application will prompt you to save your work.
If you select "Yes" then a dialog box will pop-up to assist you in saving your work to a
file in the directory of your choice. If you select "No" the application will close the
problem without saving any of your work.
		</p>
<br>
<a name="How to Cross Two Organisms"></a><font color="purple"><i>How to Cross Two Organisms</i></font>
<br>
<p ><img src="../images/cross.gif">To cross two organisms you first need to select a male organism and a 
female organism from any of the open cages (the male organism and the female organism
can be from different cages). To cross these to organisms and create the set of offsprings
that they would produce, select "Cross Two" from the "Utilities" menu or click on the
"Cross" button on the toolbar. This will create a new cage containing the set of 
offsprings of the two parents used in the cross.
		</p>
<br>

<a name="How to Print"></a><font color=purple><i>How to Print the work you have done so far</i></font>
<br>
<p><img src="../images/print.gif">To print the field population (Cage 1) and all the cages you have
generated so far, either click the Print button (shown at left), or select "Print Work" from the "File"
menu. You may need to set up the printer first; you do this by selecting "Page Setup" from the "File"
menu.
</p>
<br>

<a name="How to Print to File"></a><font color="purple"><i>How to Print to File</i></font>
<br>
<p ><img src="../images/printtofile.gif">You can use this feature to store your work into a 
file in printer friendly format; this file can be displayed in any web-browser and many word
processors. 
To print to a file select "Print To File" from the "File" menu or click on the "Print to
File" button on the toolbar. This will open up a Dialog window to allow you to give the
file a name and destination of your choice. Once you have given the file a name and
decided on the location click on the "Print" button. Your work will be saved in a 
printer friendly format into a file. The file will have a .html extension.
		</p>
<br>

<a name="Summarize Cages"></a><font color="purple"><i>How to summarize the results from a set of cages
</i></font>
<br>
<p>By selecting one or more Cages and choosing &quot;Create Summary Chart&quot; from the Utilities menu, you can 
have VGLII count the number of each type of organism found in the selected set of Cages.<p>
First, double-click on each of the cages to select them for summarization; they will turn light
yellow to show that they are selected.  You can unselect selected cages by double-clicking on them; you 
can unselect all cages by choosing &quot;Unselect All&aquot; from the Utilities menu.<p>
Once you have selected a set of Cages, choose &quot;Create Summary Chart&quot; from the Utilities menu and you
will see something like this:<p>
<img src="fig5.jpg"><br>
The top line shows that this was a summary of cages 7, 8, 9, 10, &amp; 11.<br>
These were produced from crosses of two heterozygous parents; thus, we would expect a 3:1 ratio.<br>
The observed ratio 120:26 is very close.<br>
You can choose which Characters to summarize by selecting the appropriate Characters at the top
of the window.
<br>
<a name="Close/Re-open Cages"></a><font color="purple"><i>Close/Re-open Cages</i></font>
<br>
<p >You can use this feature to close/re-open any of the cages you have created till now.
Select "Cages" from the "Utilities" menu. A window will pop-up with the list of all
the cages you have created till now. The ones which are currently visible will be checked
on the rest will be check-off. Click on the "Visibility" option beside each Cage listing
to make that Cage visible/invisible.
		</p>
<br>
<a name="Re-arrange Cages"></a><font color="purple"><i>Re-arrange Cages</i></font>
<br>
<p >You can use this feature to re-arrange the cages you have created in an orderly fashion.
Select "Re-arrange Cages" from the "Utilities" menu. All the cages that are currently
visible will be lined up one below the other and left to right.
		</p>
<br>

<a name="How to Get Details about each Phenotype"></a><font color="purple"><i>How to Get Details about each Phenotype</i></font>
<br>
<p >To get more details and a detailed diagram about the phenotype of organisms in a cage,
you can click on the image of the phenotype shown in the cage. This will pop-up a bigger
and more detailed image of the organism highlighting the phenotype in question. Note that
these images are rather primitive; they are only designed to illustrate what the combined
phenotype <i>might</i> look like. One is shown below:<p>
<center><img src="fig6.jpg"></center>
		</p>
<br>
<a name="How to Get Details about VGLII"></a><font color="purple"><i>How to Get Details about VGL</i></font>
<br>
<p ><img src="../images/about.gif">To get more details about the VGLII application you can select "About VGLII"
 from the "Help"
menu or simply click on the "About VGL" button. This will pop-up an information window.
		</p>

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